I had an issue in 2017 with Orbitz where I got no notification of a flight being canceled, after calling to check my flight status 2 weeks out, I was just told that an agent tried to call me and got a busy signal (not sure how that happens on a cell phone). They tried to book me on a much worse flight on different days, I canceled and booked straight through the airline and never booked a flight through an OTA again after that for personal travel. For hotels though, I book through OTAs all the time and never had an issue in Japan or anywhere else.